Dr. Percival "Perry" Ulysses Cox is portrayed by John C. McGinley and appears in 178 episodes of Scrubs, where he was a main character for all nine seasons. He first appears in the pilot episode "My First Day" and last appears in the series finale "Our Thanks". It is assumed he is still Chief of Medicine at New Sacred Heart.

Perry Cox is the Chief of Medicine and Attending Physician at New Sacred Heart Hospital. He is also currently teaching at Winston University. Dr. Cox worked at Sacred Heart Hospital for many years and educated many interns and residents through his tough-love style. He quickly became J.D.'s reluctant mentor, although he didn't permit use of the term.

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Cox is a senior attending physician at Sacred Heart Hospital and is also the Chief of Medicine for the hospital. Dr. Cox is around 47 years old, and of Irish descent. ("My Friend the Doctor") He is the sarcastic, bitter mentor of J.D.. Cox routinely rants at and belittles J.D., though his apparently rough treatment of him is intended as conditioning for the rigors and horrors of hospital life, as well as an outlet for Dr. Cox's frustration in his personal life. He is secretly proud of J.D. and thinks he has the potential to become an incredible doctor. He was promoted to Chief of Medicine after Bob Kelso recommended him for the job. He was reluctant to take it at first, but when he realized he likes hating people and everybody already hated him, he was fine with accepting the job. ("My Cookie Pants") Although the new job is demanding, he tries to do everything it requires and see some patients. This is very difficult and he occasionally forgets to do things. ("My New Role")("My Lawyer's in Love")

As a professor, he views all of his students as murderers and assassins who will try their hardest to kill his patients. He is very aggressive toward them and tries to weed out the weak. He has taken a liking to Drew, and because of this he has set his expectations for him very high. ("Our Drunk Friend")

Cox's family is from Pittsburgh. He has a sister Paige, who is a born-again Christian. His father was an abusive alcoholic and his mother did nothing to prevent this behavior. Perry's abusive and traumatic childhood could help explain his intimacy issues and his marriage to Jordan. According to Carla, both of his parents lacked parenting skills, and he might have murdered them. ("My Saving Grace")

Cox has two children by Jordan - a son, Jack, and a daughter, Jennifer Dylan. He has had a vasectomy, reversed it and then had another vasectomy, but it didn't take. He is very dedicated to his job and sometimes it takes a toll on him. He is also very conscious about his body, and works out quite often.

Dr. Cox is the reluctant mentor of J.D.. He met J.D. on his first day as an intern, and has constantly been abrasive and sarcastic with him. ("My First Day") He rarely calls J.D. by his real name, but rather by a girl's name or Newbie. This is his tough-love approach to teaching, but even when they are outside of the hospital, he continues the same mean mannerisms. When his harshness seems to put a little too much pressure on J.D., Cox knows when to lay off and has from time to time been supportive. Also, when J.D.'s father, Sam Dorian, passes away, Cox comforts him in his time of sadness. ("My Cake") He is not, however, a very good ear to listen to J.D.'s problems, for he doesn't seem to care about his personal life, and often mentions that he has enough problems of his own. Following Cox's promotion to Chief of Medicine, J.D. takes up the job of the guy who nags him to get things done around the hospital, and is seemingly successful in these endeavors. ("My New Role")("Their Story II") When J.D. announced that he was leaving Sacred Heart, Cox initially looked happy, but Elliot deducted that he was actually upset that J.D. leaving after all of the years he helped teach him. ("My Chief Concern") It is only in ("My Finale") that it is revealed how Dr Cox honestly feels about J.D. After J.D leaves the room, an intern begins to insult J.D, causing Dr. Cox to tell her that he is the best doctor to go through the hospital because of how much he cared, and that he was not only an extraordinary physician but also an extraordinary person. He counts his protégé as a friend. However, it turns out J.D planned with the intern to insult him in order to anger Dr. Cox, and after J.D hugs Dr. Cox and leaves, Dr. Cox tells the intern "You do realize he can go, but you have to stay?" in a threatening manner.

Jordan Sullivan and Perry have divorced, but have two children and live together. After they divorced, Jordan would use Perry for booty calls. When one of their booty calls ended with Jordan getting pregnant, they started living together again to be supportive of the child and each other. They are verbally sharp with each other, often insulting each others' sexualities and peculiarities. Although they are not married (and have no desire to be married), it can't be argued that they do not love each other. One reason they work so well together is because they are each other's equals in every way. Recently Perry has begun to refer to Jordan as his wife again although it is unclear if they've remarried.

Robert Kelso and Dr. Cox had a rivalry that, at times, affects the entire hospital. Since Dr. Kelso left, the two have bonded a little more and Cox often turns to Kelso for advice. Dr. Cox is not very fond of Dr. Kelso thinking about the patients solely by their insurance or pocketbooks. Dr. Cox often yells and rants at Kelso about making staff cutbacks or new rules, but when Dr. Kelso explains his motivation, he has no choice but to live with them. When Dr. Kelso was yelling at Elliot, Dr. Cox punched him in the face, making his nose squeak for a while. ("My Dream Job") After Kelso retired, Dr. Cox has turned to him for advice occasionally, and has even admitted that Dr. Kelso was decent at his job. ("My Saving Grace") The two now hang out and share beers and talk about the demands of the Chief of Medicine position. ("My New Role")

Dr. Cox gets extremely annoyed by Elliot Reid personally and professionally, but knows she is a talented doctor. Dr. Cox has snubbed Elliot as a mentor as much as he has snubbed J.D., but she doesn't seek his approval as much as she does her parents'. He calls her "Barbie" due to her blonde hair and sometimes ditsy mannerisms. He never had any big problems with Elliot until she decided to go into private practice. From then on he didn't respect her for her decision, but Elliot stands by her decision.

Dr. Cox used to have a crush on Carla Espinosa, but now sees her as one of the only people in Sacred Heart he can stand. Perry sees her as strong willed and empowered, which are factors he needs to see in a woman he wants to date. He seemingly only had feelings for her because he was in denial about his feelings for Jordan. However, when she married Turk, he didn't do anything to stop it because he had Jordan. Cox still turns to Carla when he needs advice, and although she doesn't always feel comfortable listening to some of his thoughts, she is there for him. Carla is also, behaving as a mother figure to J.D, Elliot, Turk and occasionally others will stand up to Cox on their behalf. As he said himself "Actually she completely gets me which is why I've been trying to drive her away", stating that she understands how he feels about himself, others, his job and his mannerisms.

Dr. Cox puts up with Christopher Turk. Because he usually sees Turk when he is with J.D., he isn't fond of their antics. He has sized up Turk, but has also helped him work out. ("My Drug Buddy") ("My Sacrificial Clam"). He sometimes asks Turk to be a surgical consultant, noting once that, in his opinion, Turk is actually smarter than most of the other surgeons, while on another occasion he asked Turk to be present when his unborn daughter needed surgery when Perry couldn't be there himself. They also shared a pee-schedule together. He also plays games with Turk such as Smelly Belly, and Hands on a Coma Patient. He says it's because they're men and that's what men do.

Although Dr. Cox doesn't respect Janitor for his profession, they often share moments together. Janitor is one of the few people that doesn't fear Dr. Cox. Both Janitor and Dr. Cox seem to be annoyed by J.D., with Janitor even helping Dr. Cox catch J.D, and they share their thoughts sometimes. They don't talk much inside the hospital, to keep up the Janitor's street cred, but they were bar buddies for a while. They are both experts on "hating people", and seem to have a mutual respect for this fact. ("My ABC's") According to Carla, both of them are "borderline psychotics who hate everyone."

Perry doesn't support the religious choices Paige makes, but still loves her as a sister. He and Paige have a hostile and difficult relationship, ostensibly because neither can appreciate the religious and scientific viewpoints held by the other. It was ultimately revealed that Paige's presence reminded Cox of the troubled childhood that he consistently tried to forget.

Dr. Cox's best friend Ben Sullivan was also his ex-brother-in-law. Ben and Perry enjoyed hugging each other for uncomfortably long periods of time and playing "gay chicken". They are the definition of two best friends. When Ben was diagnosed with leukemia, Perry took the news pretty hard, unfairly blaming J.D. for it. When Ben passed away, Perry was depressed for a short time, but soon got over his mourning, and, supposedly, he even apologized to J.D. for unfairly blaming him for Ben's death.

Drew is Dr. Cox's favorite medical student, but he has huge expectations for him. As a sort of twisted affection, Perry demands that Drew constantly prove that Drew is his #1 student by wearing a pink #1 shirt and answering the ridiculously difficult questions. By this, he is also alienating Drew from his classmates.

Being referred to by certain names such as "Big Cheese," "Chief Dr. Cox" or "Dr. Professor Cox".

Drew

Flicking the dead

Giving rants

He used to like to hike but Jordan got that in the divorce ("My Occurrence")

His thesaurus

Jerome Bettis

Lee Marvin Movies

Lindsay Lohan

Scotch on the rocks (The Janitor drinks some of his scotch once and remarks "Black Label"; that coupled with the bottle of scotch in Cox's office in Season 9, it is safe to assume that Dr. Cox's favorite scotch is Johnnie Walker Black Label)

Sports (Detroit Red Wings, Pittsburgh Steelers)

The gays; their music, their sense of style, what they've done with Halloween

“I suppose I could riff a list of things that I care as little about as our last week together. Lemme see, uhh.... Low-carb diets. Michael Moore. The Republican National Convention. Kabbalah and all Kabbalah-related products. Hi-def TV, the Bush daughters, wireless hot spots, 'The O.C.', the U.N., recycling, getting Punk'd, Danny Gans, the Latin Grammys, the real Grammys. Jeff, that Wiggle who sleeps too darn much! The Yankees payroll, all the red states, all the blue states, every hybrid car, every talk show host! Everything on the planet, everything in the solar system, everything everything everything everything everything everything--eve--everything that exists -- past, present and future, in all discovered and undiscovered dimensions. Oh! And Hugh Jackman. Eh.”— Dr. Cox("My Old Friend's New Friend")

Dr. Cox gives out nicknames more than anybody else at Sacred Heart. He uses them as insults most often, and other times he just can't remember peoples names. No fellow staff member or patient is immune from his nicknames. In addition to giving out nicknames, Perry has been on the receiving end. Some people parody his tendency to use insulting nicknames by calling him a common name he's called them, such as J.D. calling him a girl's name. Jordan in particular likes to mock him about his first name "Perry".

He does not have a nickname such as "Q-tip" or "Blonde Doctor" that sticks with him for long.

Ever since he became chief of medicine, on Rateyourdoc.org his rating has rocketed to 9999 Stars

Is a registered Independent.

Dr. Cox's seemingly irrational hatred of Hugh Jackman in particular is a development inside joke. McGinley has stated in one of the DVD commentaries that he feels Jackman is a much more talented actor than he is, which makes him feel jealous.

Both of Dr. Cox's children have birthdays in close proximity to the death of a close friend. Jack Cox was born almost exactly one year before the death of Cox's best friend and ex-brother-in-law Ben Sullivan, and Laverne Roberts died around the same time that Jennifer Dylan Cox was born.

When Dr. Cox becomes chief of medicine he is seen to have a red swingline stapler on his desk, a reference to the movie Office Space, in which McGinley played a part in.

In the original script for "My First Day" his first name was Phil, by the time of filming his first name is Paul, his name can be seen on his name tag. For unknown reasons however these were changed and we learn his name is Perry in the episode "My Bad".